Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 5JZKZ

Calculation Name: 2WS9-3-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WS9

Chain ID: 3

ChEMBL ID:

UniProt ID: B9VV85

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2249838.637214
FMO2-HF: Nuclear repulsion 2164902.245615
FMO2-HF: Total energy -84936.391599
FMO2-MP2: Total energy -85185.139806


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(3:1:ALA)


Summations of interaction energy for fragment #1(3:1:ALA)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
0.4121.317-0.007-0.376-0.5220.001
Interaction energy analysis for fragmet #1(3:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.006
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
333ILE00.0270.0043.9140.0420.947-0.007-0.376-0.5220.001
434ARG10.9360.9696.2510.5550.5550.0000.0000.0000.000
535VAL00.0220.0178.256-0.083-0.0830.0000.0000.0000.000
636VAL0-0.023-0.02011.8240.0920.0920.0000.0000.0000.000
737SER00.0040.00715.358-0.029-0.0290.0000.0000.0000.000
838VAL00.0100.01518.4780.0150.0150.0000.0000.0000.000
939PRO0-0.002-0.00321.3810.0070.0070.0000.0000.0000.000
10310GLU-1-0.886-0.95524.438-0.073-0.0730.0000.0000.0000.000
11311SER0-0.071-0.04521.734-0.008-0.0080.0000.0000.0000.000
12312ASP-1-0.888-0.92023.205-0.063-0.0630.0000.0000.0000.000
13313SER0-0.086-0.04525.4090.0070.0070.0000.0000.0000.000
14314PHE0-0.005-0.01928.014-0.006-0.0060.0000.0000.0000.000
15315MET0-0.009-0.00527.435-0.008-0.0080.0000.0000.0000.000
16316SER00.0410.01731.251-0.005-0.0050.0000.0000.0000.000
17317SER0-0.046-0.01932.9590.0010.0010.0000.0000.0000.000
18318VAL00.0320.02527.573-0.002-0.0020.0000.0000.0000.000
19319PRO0-0.045-0.02328.8530.0010.0010.0000.0000.0000.000
20320ASP-1-0.873-0.91623.784-0.174-0.1740.0000.0000.0000.000
21321ASN0-0.116-0.07024.9120.0170.0170.0000.0000.0000.000
22322SER00.0160.01025.584-0.004-0.0040.0000.0000.0000.000
23323THR00.0160.00422.756-0.006-0.0060.0000.0000.0000.000
24324PRO0-0.0120.00224.2700.0130.0130.0000.0000.0000.000
25325LEU00.021-0.00625.404-0.003-0.0030.0000.0000.0000.000
26326TYR0-0.027-0.01228.0970.0060.0060.0000.0000.0000.000
27327PRO00.0230.00027.2870.0000.0000.0000.0000.0000.000
28328LYS10.9370.96128.5900.0910.0910.0000.0000.0000.000
29329VAL00.0460.03732.4480.0040.0040.0000.0000.0000.000
30330VAL0-0.006-0.00135.700-0.002-0.0020.0000.0000.0000.000
31331VAL0-0.0060.00637.9560.0040.0040.0000.0000.0000.000
32332PRO00.0330.02540.437-0.001-0.0010.0000.0000.0000.000
33333PRO00.0020.00544.010-0.002-0.0020.0000.0000.0000.000
34334ARG10.8990.92941.4340.0560.0560.0000.0000.0000.000
35335GLN00.0580.01047.998-0.002-0.0020.0000.0000.0000.000
36336VAL0-0.0340.00549.7840.0010.0010.0000.0000.0000.000
37337PRO00.0280.00651.962-0.001-0.0010.0000.0000.0000.000
38338GLY00.0360.02054.3310.0000.0000.0000.0000.0000.000
39339ARG10.9340.97543.7310.0520.0520.0000.0000.0000.000
40340PHE00.0160.02149.5440.0000.0000.0000.0000.0000.000
41341THR0-0.047-0.04445.499-0.001-0.0010.0000.0000.0000.000
42342ASN00.0500.02645.756-0.001-0.0010.0000.0000.0000.000
43343PHE00.0630.02746.4510.0020.0020.0000.0000.0000.000
44344ILE00.0170.00650.1330.0020.0020.0000.0000.0000.000
45345ASP-1-0.867-0.93550.756-0.041-0.0410.0000.0000.0000.000
46346VAL00.0000.00653.0540.0020.0020.0000.0000.0000.000
47347ALA00.0120.01454.7720.0020.0020.0000.0000.0000.000
48348LYS10.8120.90953.1770.0390.0390.0000.0000.0000.000
49349GLN0-0.083-0.02954.5550.0010.0010.0000.0000.0000.000
50350THR0-0.023-0.01558.4150.0010.0010.0000.0000.0000.000
51351TYR0-0.0140.02860.9810.0000.0000.0000.0000.0000.000
52352SER0-0.056-0.02962.2820.0000.0000.0000.0000.0000.000
53353PHE00.009-0.00464.5740.0000.0000.0000.0000.0000.000
54354CYS0-0.0120.00166.597-0.001-0.0010.0000.0000.0000.000
55355SER0-0.038-0.02467.6330.0000.0000.0000.0000.0000.000
56356ILE00.0340.03169.5840.0000.0000.0000.0000.0000.000
57357SER0-0.0160.00072.8570.0010.0010.0000.0000.0000.000
58358GLY0-0.009-0.00171.4980.0010.0010.0000.0000.0000.000
59359LYS10.8670.93472.5790.0150.0150.0000.0000.0000.000
60360PRO00.0020.01471.0210.0000.0000.0000.0000.0000.000
61361TYR0-0.024-0.03072.2930.0000.0000.0000.0000.0000.000
62362PHE00.0570.03475.1980.0000.0000.0000.0000.0000.000
63363GLU-1-0.796-0.88877.848-0.013-0.0130.0000.0000.0000.000
64364VAL00.0490.04181.6390.0000.0000.0000.0000.0000.000
65365THR00.0390.00084.5860.0000.0000.0000.0000.0000.000
66366ASN00.0410.03688.1830.0000.0000.0000.0000.0000.000
67367THR0-0.034-0.01590.4190.0000.0000.0000.0000.0000.000
68368SER0-0.049-0.04986.0190.0000.0000.0000.0000.0000.000
69369GLY00.0020.01987.3890.0000.0000.0000.0000.0000.000
70370ASP-1-0.793-0.88985.520-0.013-0.0130.0000.0000.0000.000
71371GLU-1-0.863-0.92083.351-0.013-0.0130.0000.0000.0000.000
72372PRO0-0.043-0.01577.9830.0000.0000.0000.0000.0000.000
73373LEU0-0.031-0.02479.7700.0000.0000.0000.0000.0000.000
74374PHE0-0.048-0.02670.2120.0000.0000.0000.0000.0000.000
75375GLN00.0530.02672.7190.0000.0000.0000.0000.0000.000
76376MET0-0.0230.00966.7220.0000.0000.0000.0000.0000.000
77377ASP-1-0.822-0.90766.283-0.018-0.0180.0000.0000.0000.000
78378VAL0-0.045-0.02363.009-0.001-0.0010.0000.0000.0000.000
79379SER00.024-0.01560.362-0.001-0.0010.0000.0000.0000.000
80380LEU0-0.001-0.00956.9980.0010.0010.0000.0000.0000.000
81381SER0-0.0030.00258.7740.0000.0000.0000.0000.0000.000
82382ALA0-0.0030.01760.9240.0010.0010.0000.0000.0000.000
83383ALA00.0660.03164.6020.0000.0000.0000.0000.0000.000
84384GLU-1-0.861-0.95066.677-0.018-0.0180.0000.0000.0000.000
85385LEU00.009-0.00162.0990.0000.0000.0000.0000.0000.000
86386HIS00.0060.02662.583-0.001-0.0010.0000.0000.0000.000
87387GLY0-0.003-0.00362.2340.0000.0000.0000.0000.0000.000
88388THR0-0.058-0.03861.783-0.001-0.0010.0000.0000.0000.000
89389TYR00.0630.01953.916-0.001-0.0010.0000.0000.0000.000
90390VAL00.0350.01257.122-0.001-0.0010.0000.0000.0000.000
91391ALA00.0470.04456.682-0.001-0.0010.0000.0000.0000.000
92392SER0-0.002-0.01056.6030.0000.0000.0000.0000.0000.000
93393LEU0-0.071-0.01350.748-0.001-0.0010.0000.0000.0000.000
94394SER00.015-0.03652.153-0.002-0.0020.0000.0000.0000.000
95395SER0-0.035-0.00952.537-0.001-0.0010.0000.0000.0000.000
96396PHE00.0120.02548.1640.0000.0000.0000.0000.0000.000
97397PHE0-0.021-0.01445.847-0.003-0.0030.0000.0000.0000.000
98398ALA00.0430.03148.1350.0020.0020.0000.0000.0000.000
99399GLN0-0.034-0.01648.8590.0000.0000.0000.0000.0000.000
1003100TYR00.0290.01450.788-0.002-0.0020.0000.0000.0000.000
1013101ARG10.8100.88551.8850.0380.0380.0000.0000.0000.000
1023102GLY00.0320.02154.404-0.001-0.0010.0000.0000.0000.000
1033103SER0-0.044-0.04857.2510.0010.0010.0000.0000.0000.000
1043104LEU0-0.003-0.00559.595-0.001-0.0010.0000.0000.0000.000
1053105ASN00.0100.01362.3700.0010.0010.0000.0000.0000.000
1063106PHE00.0410.02264.7660.0000.0000.0000.0000.0000.000
1073107ASN0-0.063-0.02967.3230.0010.0010.0000.0000.0000.000
1083108PHE00.0320.01670.2750.0000.0000.0000.0000.0000.000
1093109ILE00.0250.00271.7330.0000.0000.0000.0000.0000.000
1103110PHE0-0.0040.00575.7780.0000.0000.0000.0000.0000.000
1113111THR0-0.048-0.03177.7920.0000.0000.0000.0000.0000.000
1123112GLY00.0120.00880.7930.0000.0000.0000.0000.0000.000
1133113ALA00.0070.00484.4130.0000.0000.0000.0000.0000.000
1143114ALA00.028-0.00486.5990.0000.0000.0000.0000.0000.000
1153115ALA0-0.0140.01387.6770.0000.0000.0000.0000.0000.000
1163116THR0-0.039-0.03787.0490.0000.0000.0000.0000.0000.000
1173117LYS10.8090.88586.9870.0140.0140.0000.0000.0000.000
1183118ALA00.0440.01684.7960.0000.0000.0000.0000.0000.000
1193119LYS10.8620.92684.3720.0140.0140.0000.0000.0000.000
1203120PHE00.0060.00279.7720.0000.0000.0000.0000.0000.000
1213121LEU00.0220.01778.6950.0000.0000.0000.0000.0000.000
1223122VAL0-0.007-0.00273.5280.0000.0000.0000.0000.0000.000
1233123ALA00.0360.00674.6680.0000.0000.0000.0000.0000.000
1243124PHE00.0070.00566.3320.0000.0000.0000.0000.0000.000
1253125VAL0-0.004-0.00670.9730.0000.0000.0000.0000.0000.000
1263126PRO00.0410.02468.4780.0000.0000.0000.0000.0000.000
1273127PRO00.009-0.00365.4890.0010.0010.0000.0000.0000.000
1283128HIS00.0220.01368.6180.0000.0000.0000.0000.0000.000
1293129SER0-0.043-0.04271.9890.0000.0000.0000.0000.0000.000
1303130ALA00.000-0.00874.0100.0000.0000.0000.0000.0000.000
1313131ALA00.0400.04873.7460.0000.0000.0000.0000.0000.000
1323132PRO0-0.054-0.00775.4210.0010.0010.0000.0000.0000.000
1333133LYS10.8590.88778.3080.0130.0130.0000.0000.0000.000
1343134THR00.011-0.00281.0250.0000.0000.0000.0000.0000.000
1353135ARG10.7430.80581.6540.0130.0130.0000.0000.0000.000
1363136ASP-1-0.813-0.87682.343-0.013-0.0130.0000.0000.0000.000
1373137GLU-1-0.782-0.85880.727-0.014-0.0140.0000.0000.0000.000
1383138ALA0-0.002-0.00677.9640.0000.0000.0000.0000.0000.000
1393139MET0-0.042-0.01078.2290.0000.0000.0000.0000.0000.000
1403140ALA0-0.024-0.00879.4100.0000.0000.0000.0000.0000.000
1413141CYS0-0.069-0.01674.3030.0000.0000.0000.0000.0000.000
1423142ILE00.0240.01369.8520.0000.0000.0000.0000.0000.000
1433143HIS0-0.026-0.01973.6260.0000.0000.0000.0000.0000.000
1443144ALA0-0.0100.00675.2470.0000.0000.0000.0000.0000.000
1453145VAL00.0100.00077.1150.0000.0000.0000.0000.0000.000
1463146TRP0-0.032-0.01977.6360.0000.0000.0000.0000.0000.000
1473147ASP-1-0.769-0.86580.398-0.014-0.0140.0000.0000.0000.000
1483148VAL00.0690.03781.7450.0000.0000.0000.0000.0000.000
1493149GLY0-0.019-0.01483.0120.0000.0000.0000.0000.0000.000
1503150LEU0-0.0350.01282.4610.0000.0000.0000.0000.0000.000
1513151ASN0-0.003-0.01878.234-0.001-0.0010.0000.0000.0000.000
1523152SER00.0040.00579.5600.0000.0000.0000.0000.0000.000
1533153ALA00.0110.00474.4240.0000.0000.0000.0000.0000.000
1543154PHE00.0020.01074.5990.0000.0000.0000.0000.0000.000
1553155SER00.001-0.01368.5970.0000.0000.0000.0000.0000.000
1563156PHE0-0.001-0.00469.5260.0000.0000.0000.0000.0000.000
1573157ASN0-0.035-0.03262.9690.0000.0000.0000.0000.0000.000
1583158VAL00.0210.01564.6430.0010.0010.0000.0000.0000.000
1593159PRO00.0170.01263.609-0.001-0.0010.0000.0000.0000.000
1603160TYR0-0.006-0.02155.9380.0000.0000.0000.0000.0000.000
1613161SER0-0.055-0.04761.1280.0010.0010.0000.0000.0000.000
1623162SER00.024-0.00758.1940.0010.0010.0000.0000.0000.000
1633163PRO0-0.020-0.00258.818-0.001-0.0010.0000.0000.0000.000
1643164ALA00.0360.02754.077-0.001-0.0010.0000.0000.0000.000
1653165ASP-1-0.837-0.89551.440-0.036-0.0360.0000.0000.0000.000
1663166PHE0-0.037-0.03048.725-0.002-0.0020.0000.0000.0000.000
1673167MET00.0060.06752.9970.0010.0010.0000.0000.0000.000
1683168ALA0-0.005-0.00953.631-0.002-0.0020.0000.0000.0000.000
1693169VAL0-0.033-0.01652.9940.0010.0010.0000.0000.0000.000
1703170TYR0-0.039-0.02452.1070.0020.0020.0000.0000.0000.000
1713171SER0-0.024-0.02556.1700.0000.0000.0000.0000.0000.000
1723172ALA0-0.008-0.01058.6680.0000.0000.0000.0000.0000.000
1733173GLU-1-0.912-0.95560.737-0.016-0.0160.0000.0000.0000.000
1743174ALA0-0.025-0.01261.991-0.001-0.0010.0000.0000.0000.000
1753175THR00.0460.02857.5570.0000.0000.0000.0000.0000.000
1763176VAL0-0.034-0.02958.4300.0000.0000.0000.0000.0000.000
1773177VAL00.014-0.00754.840-0.001-0.0010.0000.0000.0000.000
1783178ASN0-0.0040.00757.4300.0000.0000.0000.0000.0000.000
1793179VAL00.0080.01059.4280.0000.0000.0000.0000.0000.000
1803180SER00.018-0.00461.6830.0000.0000.0000.0000.0000.000
1813181GLY0-0.0120.00463.5290.0000.0000.0000.0000.0000.000
1823182TRP0-0.047-0.02767.3570.0000.0000.0000.0000.0000.000
1833183LEU0-0.036-0.00568.9330.0000.0000.0000.0000.0000.000
1843184GLN00.0150.00370.8400.0000.0000.0000.0000.0000.000
1853185VAL0-0.042-0.02974.4920.0000.0000.0000.0000.0000.000
1863186TYR00.006-0.00777.1460.0000.0000.0000.0000.0000.000
1873187ALA00.004-0.00580.9280.0000.0000.0000.0000.0000.000
1883188LEU0-0.027-0.00683.4230.0000.0000.0000.0000.0000.000
1893189THR0-0.038-0.03385.6120.0000.0000.0000.0000.0000.000
1903190ALA0-0.0040.00987.0680.0000.0000.0000.0000.0000.000
1913191LEU0-0.059-0.01886.6580.0000.0000.0000.0000.0000.000
1923192THR00.0230.00389.0570.0000.0000.0000.0000.0000.000
1933193SER00.012-0.00990.9250.0000.0000.0000.0000.0000.000
1943194THR0-0.027-0.01293.2330.0000.0000.0000.0000.0000.000
1953195ASP-1-0.839-0.92595.060-0.010-0.0100.0000.0000.0000.000
1963196ILE0-0.021-0.00193.3850.0000.0000.0000.0000.0000.000
1973197ALA0-0.008-0.00194.6370.0000.0000.0000.0000.0000.000
1983198VAL0-0.051-0.01592.6370.0000.0000.0000.0000.0000.000
1993199ASN0-0.059-0.03789.514-0.001-0.0010.0000.0000.0000.000
2003200SER00.0230.02691.3410.0000.0000.0000.0000.0000.000
2013201LYS10.8470.88485.1600.0120.0120.0000.0000.0000.000
2023202GLY00.0190.01784.8100.0000.0000.0000.0000.0000.000
2033203ARG10.8140.90579.4860.0140.0140.0000.0000.0000.000
2043204VAL00.0290.01775.8430.0000.0000.0000.0000.0000.000
2053205LEU00.0020.00573.4250.0000.0000.0000.0000.0000.000
2063206VAL00.0110.00570.3570.0000.0000.0000.0000.0000.000
2073207ALA0-0.0090.00167.3020.0000.0000.0000.0000.0000.000
2083208VAL0-0.004-0.00163.2040.0000.0000.0000.0000.0000.000
2093209SER00.002-0.01961.3570.0000.0000.0000.0000.0000.000
2103210ALA0-0.006-0.00257.2070.0000.0000.0000.0000.0000.000
2113211GLY00.0170.01959.2790.0000.0000.0000.0000.0000.000
2123212PRO0-0.012-0.01657.904-0.001-0.0010.0000.0000.0000.000
2133213ASP-1-0.819-0.88855.615-0.033-0.0330.0000.0000.0000.000
2143214PHE0-0.0320.00354.698-0.001-0.0010.0000.0000.0000.000
2153215SER0-0.023-0.02249.429-0.002-0.0020.0000.0000.0000.000
2163216LEU00.0280.01849.5890.0020.0020.0000.0000.0000.000
2173217ARG10.8580.93845.9790.0410.0410.0000.0000.0000.000
2183218HIS00.006-0.01043.7360.0010.0010.0000.0000.0000.000
2193219PRO00.0330.02042.3360.0020.0020.0000.0000.0000.000
2203220VAL0-0.030-0.02844.105-0.001-0.0010.0000.0000.0000.000
2213221ASP-1-0.914-0.94243.438-0.040-0.0400.0000.0000.0000.000
2223222LEU0-0.035-0.02646.4980.0010.0010.0000.0000.0000.000
2233223PRO00.0020.01550.0450.0010.0010.0000.0000.0000.000
2243224ASP-1-0.912-0.95651.908-0.020-0.0200.0000.0000.0000.000
2253225LYS10.9090.94654.6420.0200.0200.0000.0000.0000.000
2263226GLN0-0.0120.00657.2430.0010.0010.0000.0000.0000.000